Post on 07-Apr-2016
ITRANS database Sorting structural motifs in cellular transporters
Afonso M.S. DuarteBiological Energy Transduction Lab
ITQB-UNL, Portugal
Cellular membrane transporters
Takamori et al, Cell. 2006 Nov 17;127(4):831-46
• Nutrients uptake
• “Waste disposal”
• Signal transduction
• Energy production
• Drug targets
Ion transporters
Activity
Regulation
Molecular mechanism
Protein structure at different levels
Atomic resolution
Structural motifs
Repeats
What are the basic features of repeats ?
Can repeats be systematized and characterized at sequence and
structural level?
? ? ? ? ? ?
Structural motifs and repeats
Structural motifs
Repeats
transport mechanism
inhibition
activation
Post-translational modifications
# TMs# # β
# kinks
ions
repeat orientation
Ion transporters
Charges
hydrophobicity
Itrans DB
Itrans – Data sources
Itrans DB
literature
DB of ion and small molecules transporters
with known 3D structure
Itrans – Structure
Itrans – Structure
Itrans – input
Itrans – full table
≠ query –> custom-made tables
Itrans – repeats table
Itrans – transporter entry
Itrans - Statistics
Acknowledgments ITQB-UNL
Manuela Pereira
Guilherme BeneditoJosé SilvaDalila FernandesJoana SimõesCátia CostaAna Batista Bruno Marreiros
Filipa CalistoFilipa Sena Patrícia RefojoPaulo CastroAndreia Silva